Research Highlights (15)

Part 1: Pathway engineeringIt is now accepted that fossil fuel reserves, the main source for liquid petroleum, will eventually be depleted. It is also established that the use of fossil fuels has a negative impact on the environment, contributing to global warming, through re-introduction of trapped carbon, a greenhouse gas, into the atmosphere. Thus an alternative source for liquid fuels needs to be found and one of the proposed alternatives is biofuels. Biofuels refers to technologies that employ living organisms, mostly yeast, algae or bacteria, to convert biomass to liquid fuels. Apart from the environmental benefits which come with biofuels, they may also contribute to the enhancement of energy security in countries which don’t have access to fossil fuel deposits, and offer a more profitable use of crops other than as a food source.

The ASTER™ process is commercially used to bioremediate cyanide- (CN-) and thiocyanate- (SCN-) containing waste water, typically, from cyanidation of refractory gold ores. There are currently three industrial-scale ASTER™ processes in operation worldwide. This aerobic bioprocess reduces the CN- and SCN- concentrations to below 1 mg/L in a continuous system, facilitating reuse or safe discharge of process water. To date, the microbial consortia associated with this bioprocess have been poorly characterized and, as a result, the relative abundance and diversity of the community has been significantly under-represented. Researchers within the Centre for Bioprocess Engineering Research (CeBER) at the University of Cape Town, together with those at the University of California, Berkeley are employing a molecular approach, including 16S rRNA gene surveys and metagenomic analysis, to study CN- and SCN- biodegradation within laboratory-scale reactors.

There has been growing focus on the potential to use gold nanoparticles as tools in the field of bionanotechnology because of their unique optical, electronic and molecular recognition properties. Gold nanoparticles are known to be fairly stable and are regarded as generally bio-compatible. However, some studies have reported that these nanoparticles could be toxic to some organisms, including bacteria. The mechanism by which gold nanoparticles may confer toxicity to E. coli cells remains to be fully understood.

Research into the molecular mechanisms of common yeasts and bacteria at the University of the Free State in South Africa seeks to exploit the roles of lipid molecules as instigators of disease symptoms towards development of new therapeutics and antifungal agents.

L-carnitine, a medically relevant, amino acid-derived molecule is a valuable target for biotechnological production. Researchers at the Institute for Wine Biotechnology, Stellenbosch University has recently provided the first report of a metabolically engineered carnitine producing strain of the industrial yeast, Saccharomyces cerevisiae, an organism that does not natively produce its own carnitine. This was achieved by cloning and reconstructing the Neurospora crassa L-carnitine biosynthesis pathway in the baker’s yeast to create an L-carnitine producing strain. The engineered yeast strains are able to catalyze the synthesis of L-carnitine from the pathway’s precursor, trimethyllysine, as well as from intermediates. Several native S. cerevisiae genes were identified that contribute to, or interfere with, the heterologous pathway. This includes (i) the threonine aldolase Gly1p which effectively catalyzed the second step of the pathway, fulfilling the role of a serine hydroxymethyltransferase, (ii) the arginine transporter Can1p which was identified as the yeast transporter for trimethyllysine, and (iii) the two serine hydroxymethyltransferases, Shm1p and Shm2p, which reduced the flux through the heterologous pathway. The work opens opportunities for using an engineered, L-carnitine producing S. cerevisiae strain in various industrial applications.

A plant's survival is determined by its ability to tolerate stress that arises from physical, chemical and biological events. For example, nutrient limitation affects cellular functions, and consequently, plant development. This could be due to nutrient depletion or inaccessibility as nutrients such as phosphorus and iron could be locked up in complex compounds in the soil. In addition, plants have to withstand harsh environmental conditions such as heat, winds, torrent storms and drought. Disease-causing pathogens and pesticides are another threat that reduce a plant’s fitness.

Pseudomonasaeruginosa and Staphylococcusaureus causes severe infections, especially in nosocomial environments. The cells are often deeply imbedded in biofilms, which makes treatment of the infections extremely difficult. Cells exposed to antibiotic levels below MIC (minimal inhibitory concentration) may develop resistance. The aim of this study was to develop a drug carrier that would keep antibiotic levels, in this case Ciprofloxacin, well above MIC for the duration of treatment. By electrospinning Ciprofloxacin into a nanofiber scaffold consisting of poly(D,L-lactide) (PDLLA) and poly(ethylene oxide) (PEO), the antibiotic was released within 2 h, killing 99% of P. aeruginosa and 91% of a methicillin-resistant strain of S. aureus in a biofilm. Ciprofloxacin, which remained intact, were released from the nanofibers for 7 days at levels above MIC. The nanofibers were not toxic when tested against MCF-12A breast epithelial cells. Antibiotic-filled nanofibers may be the answer to the eradication of P. aeruginosa and S. aureus biofilms.

A significant number of households in rural South Africa rely on roof-harvested rainwater (RHRW) for domestic purposes. Although, there is a general public health perception that RHRW is safe to drink, the presence of potential pathogens has been reported in this water source. Generally, the microbiological methods used to evaluate water quality depend on conventional culturing methods, which may underestimate total pathogen content and diversity and, thus limit the extent to which one can fully understand potential infectious risks from RHRW use. However, the use of high-throughput next-generation sequencing, (pyrosequencing) offers an alternative, in which detailed community structure can be achieved in combination with a fairly high taxonomic resolution. Not only does high-throughput next-generation sequencing allow for the detection and identification of dominant bacteria phylotype profiles within a sample but the high sequence numbers produced allows for the detection of rare species including pathogens within bacterial communities.

The St Lucia Estuary is part of the iSimangaliso Wetland Park, South Africa’s first UNESCO World Heritage Site, and is the largest estuarine system in Africa. This three-lake complex is particularly vulnerable to droughts and hypersaline conditions due to its large surface area (350 km2) and shallow water depth (average depth 0.9 m). A widespread bloom of the unicellular cyanobacterium Cyanothece sp. appeared in June 2009 and persisted for 18 months within the two northern basins of St Lucia (False Bay and North Lake). This was the first recorded bloom of this genus globally.

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The quality of the essential commodity water is being compromised by contaminants originating from anthropogenic sources, industrial activities, and agriculture amongst others. Water scarcity and severe drought in many regions of the world also represents a significant challenge to the availability of this resource. Domestic rainwater harvesting (DRWH), which involves the collection and storage of water from rooftops and diverse surfaces, is successfully implemented worldwide as a sustainable water supplement. In South Africa, a water-scarce country, the use of domestic rainwater harvesting is predominantly practised by communities situated in KwaZulu-Natal and the Eastern Cape. While the use of DRWH tank systems can definitely suffice and serve as an alternative water supply, there is a health risk associated with the use of this water source for drinking purposes, especially if the water is used untreated. Currently the information available on the microbial and chemical quality of harvested rainwater in South Africa is limited.

Antibiotic resistance in bacterial pathogens is a major cause of concern for modern medicine, as this renders these “miracle drugs” ineffective. The accidental discovery of penicillin in 1928 by Alexander Fleming and the countless lives saved by this antibiotic in the 1940’s pioneered modern medicine. However, injudicious use of penicillin and various other antibiotics has caused a major problem in the treatment of “once easily treatable” bacterial infections. A marked increase in antibiotic-resistant pathogens has been reported over the last few decades, including the well-known methicillin-resistant Staphylococcus aureus (MRSA). The emergence of multi-drug resistant bacteria has amplified this problem. Antibiotic resistance is causing a regression back to a “pre-antibiotic era” where a minor scrape or cut can lead to a battle between life and death. Skin is our first line of defence against the onslaught of various pathogens causing infection; it plays a role in thermoregulation and maintaining of homeostasis in addition to having immunological, neurosensory and metabolic functions. Severe skin damage, however, exposes underlying tissue to microbial invasion which can easily progress into severe life threatening infections if not treated successfully.

Very few people know that the smell from wet soil on a rainy day is due to the presence of a compound called geosmin. This compound is produced by a variety of soil dwelling actinobacterial strains. Actinobacteria are amazing microorganisms and have been exploited over the past century for their ability to produce antibiotics, enzymes, antioxidants and pigments.

The University of the Western Cape is partner of a large-scale, four-year project launched in October 2012 called PharmaSea funded by the EU. The UWC team is led by Prof Marla Tuffin, Acting Director of the Institute for Microbial Biotechnology and Metagenomics (IMBM), and in collaboration with Prof Michael Davies-Coleman.The collaborative project PharmaSea will bring European researchers to some of the deepest, coldest and hottest places on the planet. Scientists from the UK, Belgium, Norway, Spain, Ireland, Germany, Italy, Switzerland and Denmark will work together to collect and screen samples of mud and sediment from huge, previously untapped, oceanic trenches. The large-scale, four-year project is backed by more than €9.5 million of EU funding and brings together 24 partners from 14 countries from industry, academia and non-profit organisations.